GBase.h

 #ifndef G_BASE_DEFINED
 #define G_BASE_DEFINED
-#define GCLIB_VERSION "0.11.2"
+#define GCLIB_VERSION "0.11.3"
 
 #ifdef HAVE_CONFIG_H
 #include "config.h"

GVec.hh

@@ -64,7 +64,7 @@ template <class OBJ> class GVec {
     GVec(int init_count, const OBJ init_val);
     GVec(int init_count, OBJ* init_val, bool delete_initval=true); //convenience constructor for complex vectors
     GVec(const GVec<OBJ>& array); //copy constructor
-    const GVec<OBJ>& operator=(GVec<OBJ>& array); //copy operator
+    const GVec<OBJ>& operator=(const GVec<OBJ>& array); //copy operator
     virtual ~GVec();
     void Insert(int idx, OBJ item) { Insert(idx, &item); }
     void Insert(int idx, OBJ* item);
@@ -148,7 +148,7 @@ template <class OBJ> class GPVec {
     GPVec(bool free_elements);
     GPVec(GPVec<OBJ>& list); //copy constructor?
     GPVec(GPVec<OBJ>* list); //kind of a copy constructor
-    const GPVec<OBJ>& operator=(GPVec<OBJ>& list);
+    const GPVec<OBJ>& operator=(const GPVec<OBJ>& list);
     inline OBJ* Get(int i) {
     	TEST_INDEX(i);
         return fList[i];
@@ -246,7 +246,7 @@ template <class OBJ> GVec<OBJ>::GVec(const GVec<OBJ>& array) { //copy constructo
  this->fCount=array.fCount;
  }
 
-template <class OBJ> const GVec<OBJ>& GVec<OBJ>::operator=(GVec<OBJ>& array) {
+template <class OBJ> const GVec<OBJ>& GVec<OBJ>::operator=(const GVec<OBJ>& array) {
  if (&array==this) return *this;
  Clear();
  fCapacity=array.fCapacity;
@@ -580,7 +580,7 @@ template <class OBJ> GPVec<OBJ>::GPVec(GPVec* plist) { //another copy constructo
   }
 }
 
-template <class OBJ> const GPVec<OBJ>& GPVec<OBJ>::operator=(GPVec& list) {
+template <class OBJ> const GPVec<OBJ>& GPVec<OBJ>::operator=(const GPVec& list) {
  if (&list!=this) {
      Clear();
      fFreeProc=list.fFreeProc;

debian/changelog

+libgclib (0.11.3-1) unstable; urgency=medium
+
+  * New upstream version
+  * Set upstream metadata fields: Repository.
+  * Remove obsolete fields Name from debian/upstream/metadata.
+  * Add new symbols
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 07 Nov 2019 13:35:50 +0100
+
 libgclib (0.11.2-3) unstable; urgency=medium
 
   * Correct symbols file for 32 bit systems.

debian/libgclib0.symbols

 libgclib.so.0 libgclib0 #MINVER#
 * Build-Depends-Package: libgclib-dev
+ CLASSCODE_OVL_RANK@Base 0.11.3
  COLOR_buf@Base 0.11.2
  GA_flag_BAD_ALIGN@Base 0.11.2
  GA_flag_HAS_PARENT@Base 0.11.2
@@ -336,6 +337,7 @@ libgclib.so.0 libgclib0 #MINVER#
  _ZN5GPVecI9GFastaRecE15DefaultFreeProcEPv@Base 0.11.2
  _ZN5GPVecI9GXAlnInfoE15DefaultFreeProcEPv@Base 0.11.2
  _ZN6GfList8finalizeEP9GffReader@Base 0.11.2
+ _ZN6GffObj10addPaddingEii@Base 0.11.3
  _ZN6GffObj10getSplicedEP9GFaSeqGetbPiPjS3_P12GMapSegmentsb@Base 0.11.2
  _ZN6GffObj10parseAttrsERP8GffAttrsPcbb@Base 0.11.2
  _ZN6GffObj10removeAttrEPKcS1_@Base 0.11.2
@@ -345,10 +347,12 @@ libgclib.so.0 libgclib0 #MINVER#
  _ZN6GffObj10setRefNameEPKc@Base 0.11.2
  _ZN6GffObj11transferCDSEP7GffExon@Base 0.11.2
  _ZN6GffObj12getUnsplicedEP9GFaSeqGetPiP12GMapSegments@Base 0.11.2
+ _ZN6GffObj12printCDSListEP8_IO_FILE@Base 0.11.3
  _ZN6GffObj12printGxfExonEP8_IO_FILEPKcS3_bP7GffExonbbPci@Base 0.11.2
  _ZN6GffObj12printSummaryEP8_IO_FILE@Base 0.11.2
  _ZN6GffObj13expandSegmentER5GListI7GffExonEijja@Base 0.11.2
  _ZN6GffObj13printExonListEP8_IO_FILE@Base 0.11.2
+ _ZN6GffObj13removePaddingEii@Base 0.11.3
  _ZN6GffObj14decodeHexCharsEPcPKci@Base 0.11.2
  _ZN6GffObj14exonOverlapIdxER5GListI7GffExonEjjPii@Base 0.11.2
  _ZN6GffObj14removeExonAttrER7GffExonPKcS3_@Base 0.11.2

debian/upstream/metadata

-Name: gclib
+Repository: https://github.com/gpertea/gclib

gff.cpp

@@ -31,6 +31,7 @@ void gffnames_unref(GffNames* &n) {
   if (n->numrefs==0) { delete n; n=NULL; }
 }
 
+const int CLASSCODE_OVL_RANK = 15;
 int classcode_rank(char c) {
 	switch (c) {
 		case '=': return 0; //intron chain match or full exon chain match if strict matching is enabled
@@ -42,6 +43,7 @@ int classcode_rank(char c) {
 		case 'j': return 6; // multi-exon transfrag with at least one junction match
 		case 'e': return 12; // single exon transfrag partially overlapping an intron of reference (possible pre-mRNA fragment)
 		case 'o': return 14; // other generic exon overlap
+	//****  >15 = no-overlaps (not on the same strand) from here on *****
 		case 's': return 16; //"shadow" - an intron overlaps with a ref intron on the opposite strand (wrong strand mapping?)
 		case 'x': return 18; // generic overlap on opposite strand (usually wrong strand mapping)
 		case 'i': return 20; // intra-intron (transfrag fully contained within a reference intron)
@@ -2439,6 +2441,17 @@ void GffObj::printExonList(FILE* fout) {
 	}
 }
 
+void GffObj::printCDSList(FILE* fout) {
+	//print comma delimited list of CDS intervals
+	if (!hasCDS()) return;
+	GVec<GffExon> cds;
+	this->getCDSegs(cds); //also uses/prepares the CDS phase for each CDS segment
+	for (int i=0;i<cds.Count();i++) {
+		if (i>0) fprintf(fout, ",");
+		fprintf(fout, "%d-%d", cds[i].start, cds[i].end);
+	}
+}
+
 void BED_addAttribute(FILE* fout, int& acc, const char* format,... ) {
 	++acc;
 	if (acc==1) fprintf(fout, "\t");
@@ -2708,6 +2721,26 @@ char* GffObj::getUnspliced(GFaSeqGet* faseq, int* rlen, GMapSegments* seglst) {
     return unspliced;
 }
 
+ void GffObj::addPadding(int padLeft, int padRight) {
+	 this->start-=padLeft;
+	 this->end+=padRight;
+	 if (exons.Count()>0) {
+		 exons[0]->start-=padLeft;
+		 exons.Last()->end+=padRight;
+	 }
+	 covlen+=padLeft+padRight;
+ }
+
+ void GffObj::removePadding(int padLeft, int padRight) {
+	 this->start+=padLeft;
+	 this->end-=padRight;
+	 if (exons.Count()>0) {
+		 exons[0]->start+=padLeft;
+		 exons.Last()->end-=padRight;
+	 }
+	 covlen-=padLeft+padRight;
+ }
+
 char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_start, uint* cds_end,
           GMapSegments* seglst, bool cds_open) {
 	//cds_open only makes sense when CDSonly is true by overriding CDS 3'end such that the end of
@@ -2729,7 +2762,8 @@ char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_st
   if (gsubseq==NULL) {
         GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);
   }
-  if (fspan<(int)(end-start+1)) { //special case: stop coordinate was extended past the gseq length, must adjust
+  if (fspan<(int)(end-start+1)) {
+	  //special case: stop coordinate was extended past the gseq length, must adjust
      int endadj=end-start+1-fspan;
      uint prevend=end;
      end-=endadj;
@@ -2744,7 +2778,7 @@ char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_st
      }
   }
   char* spliced=NULL;
-  GMALLOC(spliced, covlen+1); //allocate more here
+  GMALLOC(spliced, covlen+1); //IMPORTANT: covlen must be correct here!
   uint g_start=0, g_end=0;
   int cdsadj=0;
   if (CDphase=='1' || CDphase=='2') {
@@ -3216,6 +3250,7 @@ void GffObj::getCDSegs(GVec<GffExon>& cds) {
        cds.Add(cdseg);
        } //for each exon
    } // + strand
+
 }
 
 //-- transcript overlap classification functions

gff.h

@@ -22,7 +22,7 @@ extern int gff_fid_exon;
 extern const uint GFF_MAX_LOCUS;
 extern const uint GFF_MAX_EXON;
 extern const uint GFF_MAX_INTRON;
-
+extern const int CLASSCODE_OVL_RANK;
 //extern const uint gfo_flag_LEVEL_MSK; //hierarchical level: 0 = no parent
 //extern const byte gfo_flagShift_LEVEL;
 
@@ -651,13 +651,18 @@ class GffExon : public GSeg {
 
   } //constructor
 
+
   GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor
-	  (*this)=ex; //use the default copy operator
-      if (ex.attrs!=NULL) {
+      (*this)=ex; //use the default (shallow!) copy operator
+      if (ex.attrs!=NULL) { //make a deep copy here
         attrs=new GffAttrs();
         attrs->copyAttrs(ex.attrs);
       }
   }
+
+  GffExon& operator=(const GffExon& o) = default; //prevent gcc 9 warnings:
+                                           //yes, I want a shallow copy here
+
   ~GffExon() { //destructor
      if (attrs!=NULL && !sharedAttrs) delete attrs;
   }
@@ -1015,6 +1020,8 @@ public:
          printGxf(fout, showCDS ? pgffBoth : pgffExon, tlabel, gfparent, cvtChars);
       }
    void printExonList(FILE* fout); //print comma delimited list of exon intervals
+   void printCDSList(FILE* fout); //print comma delimited list of CDS intervals
+
    void printBED(FILE* fout, bool cvtChars, char* dbuf, int dbuf_len);
        //print a BED-12 line + GFF3 attributes in 13th field
    void printSummary(FILE* fout=NULL);
@@ -1023,6 +1030,10 @@ public:
            uint* cds_start=NULL, uint* cds_end=NULL, GMapSegments* seglst=NULL,
 		   bool cds_open=false);
     char* getUnspliced(GFaSeqGet* faseq, int* rlen, GMapSegments* seglst=NULL);
+
+    void addPadding(int padLeft, int padRight); //change exons to include this padding on the sides
+    void removePadding(int padLeft, int padRight);
+
    //bool validCDS(GFaSeqGet* faseq); //has In-Frame Stop Codon ?
    bool empty() { return (start==0); }
 };